The Complete Chloroplast Genome of the Vietnamese Endemic Species Aquilaria banaense P.H. Hô, 1986 (Thymelaeaceae): Structure, Evolution, and Phylogeny

TL;DR

This study sequenced the chloroplast genome of Aquilaria banaense, a rare Vietnamese tree, to understand its evolution and conservation needs.

Contribution

The first complete chloroplast genome of Aquilaria banaense is reported, providing insights into its phylogeny and genetic uniqueness.

Findings

The chloroplast genome of A. banaense is 174,810 bp with a typical quadripartite structure.

Phylogenetic analysis shows A. banaense is closely related to mainland Southeast Asian species.

Unique genomic features like IR expansion and accD variant distinguish A. banaense.

Abstract

The genus Aquilaria (Thymelaeaceae) is renowned for producing agarwood, a highly valuable resinous product of significant economic and cultural value. Yet, many of its species, including the endemic Aquilaria banaense from Vietnam, face conservation challenges due to overexploitation. This study presents the first complete chloroplast (cp) genome of A. banaense to investigate its genome structure, evolutionary characteristics, and phylogenetic position. The cp genome of A. banaense was 174,810 bp, exhibiting a typical quadripartite structure with a large single‐copy (LSC) region (87,264 bp), a small single‐copy (SSC) region (3342 bp), and two inverted repeat (IR) regions (42,102 bp), encoding unique 79 protein‐coding genes, 30 tRNA genes, and four rRNA genes. Comparative analysis across Aquilaria species revealed conserved genomic features, including IR expansion into the SSC region, absence of clpP1 introns, alongside moderate nucleotide divergent regions (such as matK‐rps16, petN‐trnT‐GGU, rps4‐ndhJ, and ndhF‐rpl32) and a distinct accD variant in A. banaense. Phylogenetic reconstruction using whole cp genomes of 13 Aquilaria species placed A. banaense sister to mainland Southeast Asian species like
A. crassna
and
A. subintegra
, clearly separated from insular Southeast Asian groups. The correlation between phylogenetic structure and geographic distribution suggests that historical biogeography and ecological factors have driven lineage divergence in Aquilaria. These findings highlight the genetic distinctiveness of A. banaense and provide valuable genetic resources for species identification and conservation planning for this vulnerable species.

This study presents the first complete chloroplast genome of Aquilaria banaense, an endemic Vietnamese species, revealing its phylogenetic position within the Aquilaria genus and its biogeographic alignment with mainland Southeast Asia. Comparative analyses highlight conserved genome structure and unique long tandem repeat variations, emphasizing the need for expanded genomic data from Malesia to support conservation efforts for this endangered, agarwood‐producing genus.

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